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Thermophilic RNA Ligase from Palaeococcus pacificus + AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VUG Rnl3 Ligase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 291.15 80 mM strontium chloride hexahydrate, 20 mM magnesium chloride hexahydrate, 40 mM sodium cacodylate trihydrate pH 7.0, 20% v/v (+/-)-2-methyl-2,4-pentanediol, 12 mM spermine tetrahydrochloride
Crystal Properties Matthews coefficient Solvent content 3.05 59.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.216 α = 90 b = 98.799 β = 90 c = 142.977 γ = 90
Symmetry Space Group P 2 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2022-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953725 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.12 42.93 93.2 0.1462 14.53 13.6 65953 21.18
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 47.66 84.44 1.275 3.36 13
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.12 42.93 0.01 60794 1838 92.15 0.1908 0.1894 0.1895 0.237 0.237 27.31
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.8207 f_angle_d 0.8601 f_chiral_restr 0.0541 f_bond_d 0.0078 f_plane_restr 0.0075
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6005 Nucleic Acid Atoms Solvent Atoms 476 Heterogen Atoms 90
Software Software Software Name Purpose PHENIX refinement PHENIX refinement Zanuda data reduction XDS data scaling PHENIX phasing